motifTestR
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (13.3%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: smped
- Language: R
- Default Branch: devel
- Homepage: https://smped.github.io/motifTestR/
- Size: 8.7 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
motifTestR 
<!-- badges: end -->
The package motifTestR provides a small set of functions for analysing transcription factor binding motifs (TFBMs).
Testing for positional bias is enabled using a novel approach, and testing for enrichment relative to a set of background sequences is enabled using multiple statistical models.
Testing for positional bias is intended to be an R native alternative to CentriMo from the MEME-suite, and will detect any deviation of note from an even distribution across the width of sequences being tested, not just the centrality of motifs. Given the conventional statistical approach taken, results are easily interpretable directly through adjusted p-values. Enrichment testing follows well-worn modelling and iterative strategies, whilst offering a novel approach to selection of control, or background, sequences.
Testing similar motifs grouped together as a set of clusters is also enabled.
To install the stable version of motifTestR from Bioconductor please try the following.
r
if (!require("BiocManager")) {
install.packages("BiocManager")
}
BiocManager::install("motifTestR")
Alternatively, the latest build can be installed using
r
if (!require("BiocManager")) {
install.packages("BiocManager")
}
BiocManager::install("smped/motifTestR")
Owner
- Name: Stevie Pederson
- Login: smped
- Kind: user
- Location: Adelaide, Australia
- Company: Black Ochre Data Labs, Telethon Kids Institute
- Twitter: stevie_ped
- Repositories: 1
- Profile: https://github.com/smped
GitHub Events
Total
- Push event: 60
- Create event: 2
Last Year
- Push event: 60
- Create event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stevie Ped | s****u@g****m | 95 |
| A Wokaty | a****y@s****u | 2 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y@u****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 4,146 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: motifTestR
Perform key tests for binding motifs in sequence data
- Homepage: https://github.com/smped/motifTestR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/motifTestR/inst/doc/motifTestR.pdf
- License: GPL-3
-
Latest release: 1.4.0
published about 1 year ago